R texinfo documents are not showing up for me

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4 participants
  • Kyle Andrews
  • Liliana Marie Prikler
  • Ludovic Courtès
  • Maxime Devos
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Kyle Andrews
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K
K
Kyle Andrews wrote on 29 May 2022 17:48
(name . bug-guix)(address . bug-guix@gnu.org)
87wne4uymp.fsf@posteo.net
Dear Guix,

I see that R provides a lot of texinfo documentation, but none of it is
showing up for me in 'Emacs M-x info' or by typing 'info R'. Is this
just my setup problem or is it a wider phenomenon?

Thanks,
Kyle
L
L
Ludovic Courtès wrote on 30 May 2022 00:37
(name . Kyle Andrews)(address . kyle@posteo.net)(address . 55709@debbugs.gnu.org)
87h7587yoj.fsf@gnu.org
Hi,

Kyle Andrews <kyle@posteo.net> skribis:

Toggle quote (4 lines)
> I see that R provides a lot of texinfo documentation, but none of it is
> showing up for me in 'Emacs M-x info' or by typing 'info R'. Is this
> just my setup problem or is it a wider phenomenon?

The following Info files are provided by ‘r-minimal’:

Toggle snippet (13 lines)
$ find -L $(guix build r-minimal) -name \*.info\*
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-exts.info-1.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-admin.info.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-data.info.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-lang.info.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-intro.info.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-exts.info-3.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-exts.info.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-exts.info-2.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-ints.info.gz
/gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-FAQ.info.gz

This package is propagated by ‘r’. Thus, you can access these manuals
for instance with:

guix shell r info-reader -- info R-intro

You can replace ‘info-reader’ by ‘emacs’; the key here is that this sets
the ‘INFOPATH’ environment variable.

Does it work for you?

HTH,
Ludo’.
K
K
Kyle Andrews wrote on 31 May 2022 02:35
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 55709@debbugs.gnu.org)
87leuiwm1q.fsf@posteo.net
Hi Ludo,

I tried with both info-reader and emacs. The former (your command)
worked (yay!), while the latter (see below) errored out: saying emacs
could not be found.

guix shell r emacs -- emacs
# /gnu/store/rg8f1jd773n2l78p24m1gds3dmvcgkjq-profile/bin/emacs: error while loading shared libraries: /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0: file too short

However, I tried also with emacs-no-x and it picked up the R texinfo
manuals with no problems. I also checked the INFOPATH and saw those
files directly in there. That's certainly better than on my system where
they are not.

The first item in $(guix describe) is:

guix acb0830
branch: master
commit: acb08304c862d65679086a9f160240bfd598289d

Cheers,
Kyle

Ludovic Courtès <ludo@gnu.org> writes:

Toggle quote (34 lines)
> Hi,
>
> Kyle Andrews <kyle@posteo.net> skribis:
>
>> I see that R provides a lot of texinfo documentation, but none of it is
>> showing up for me in 'Emacs M-x info' or by typing 'info R'. Is this
>> just my setup problem or is it a wider phenomenon?
>
> The following Info files are provided by ‘r-minimal’:
>
> $ find -L $(guix build r-minimal) -name \*.info\*
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-exts.info-1.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-admin.info.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-data.info.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-lang.info.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-intro.info.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-exts.info-3.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-exts.info.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-exts.info-2.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-ints.info.gz
> /gnu/store/jwr3aajwjxwv3swdwbdxzh8ccn3mdlvz-r-minimal-4.2.0/share/info/R-FAQ.info.gz
>
> This package is propagated by ‘r’. Thus, you can access these manuals
> for instance with:
>
> guix shell r info-reader -- info R-intro
>
> You can replace ‘info-reader’ by ‘emacs’; the key here is that this sets
> the ‘INFOPATH’ environment variable.
>
> Does it work for you?
>
> HTH,
> Ludo’.
M
M
Maxime Devos wrote on 31 May 2022 10:37
(address . 55709@debbugs.gnu.org)
caaaef9ff99e311c654558d1bc245f0fb7a70171.camel@telenet.be
Kyle Andrews schreef op di 31-05-2022 om 00:35 [+0000]:
Toggle quote (2 lines)
>   # /gnu/store/rg8f1jd773n2l78p24m1gds3dmvcgkjq-profile/bin/emacs: error while loading shared libraries: /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0: file too short

Seems suspect. I'd suggest trying

guix gc --verify=contents /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30

but that fails locally, apparently no arguments are accepted,
so maybe try

guix gc --verify=contents

(Is there a method to verify and repair a _single_ store item instead of the whole store?).

Greetings,
Maxime
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L
L
Ludovic Courtès wrote on 31 May 2022 11:37
(name . Kyle Andrews)(address . kyle@posteo.net)(address . 55709@debbugs.gnu.org)
87a6ayyren.fsf@gnu.org
Hi Kyle,

Kyle Andrews <kyle@posteo.net> skribis:

Toggle quote (7 lines)
> I tried with both info-reader and emacs. The former (your command)
> worked (yay!), while the latter (see below) errored out: saying emacs
> could not be found.
>
> guix shell r emacs -- emacs
> # /gnu/store/rg8f1jd773n2l78p24m1gds3dmvcgkjq-profile/bin/emacs: error while loading shared libraries: /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0: file too short

Could you type “unset LD_LIBRARY_PATH” before this command, to be on the
safe side? Does it make a difference?

If not, what does this say:

du -L /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0

Here I get:

1044 /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0

Thanks,
Ludo’.
K
K
Kyle Andrews wrote on 2 Jun 2022 02:42
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 55709@debbugs.gnu.org)
87czfr6ggw.fsf@posteo.net
Thanks for looking into this!

Ludovic Courtès <ludo@gnu.org> writes:

Toggle quote (14 lines)
> Hi Kyle,
>
> Kyle Andrews <kyle@posteo.net> skribis:
>
>> I tried with both info-reader and emacs. The former (your command)
>> worked (yay!), while the latter (see below) errored out: saying emacs
>> could not be found.
>>
>> guix shell r emacs -- emacs
>> # /gnu/store/rg8f1jd773n2l78p24m1gds3dmvcgkjq-profile/bin/emacs: error while loading shared libraries: /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0: file too short
>
> Could you type “unset LD_LIBRARY_PATH” before this command, to be on the
> safe side? Does it make a difference?

I tried unsetting LD_LIBRARY_PATH and it made no difference.

Toggle quote (11 lines)
> If not, what does this say:
>
> du -L /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0
>
> Here I get:
>
> 1044 /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0
>
> Thanks,
> Ludo’.

For me it gave:

0 /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0

Does this mean I have some store corruption as Maxime suggested?

Thanks,
Kyle
L
L
Liliana Marie Prikler wrote on 2 Jun 2022 08:12
(address . 55709@debbugs.gnu.org)
1866a29e035be8606f940de34228ab562bb935c5.camel@ist.tugraz.at
Am Dienstag, dem 31.05.2022 um 10:37 +0200 schrieb Maxime Devos:
Toggle quote (2 lines)
> (Is there a method to verify and repair a _single_ store item instead
> of the whole store?).
I think the syntax for that'd be ‘[sudo] guix build --repair
STORE_ITEM’.

Cheers
L
L
Ludovic Courtès wrote on 2 Jun 2022 15:39
(name . Kyle Andrews)(address . kyle@posteo.net)(address . 55709@debbugs.gnu.org)
87k09zp4kl.fsf@gnu.org
Hi,

Kyle Andrews <kyle@posteo.net> skribis:

Toggle quote (6 lines)
> For me it gave:
>
> 0 /gnu/store/vncwfb53kbnyflyc1jyd2xv9sifpw202-gtk+-3.24.30/lib/libgdk-3.so.0
>
> Does this mean I have some store corruption as Maxime suggested?

Yes, that sounds likely.

Ludo’.
K
K
Kyle Andrews wrote on 5 Jun 2022 01:29
(name . Liliana Marie Prikler)(address . liliana.prikler@ist.tugraz.at)
87leucngdq.fsf@posteo.net
I had a really hard time getting ~guix gc --verify=contents,repair~ to
actually fix the problem and get commands like emacs to run.

Nothing worked until I mounted /gnu/store as read write and removed the
zeroed file completely for that particular gtk+3.24.30 folder, removed
the ~guix/store/.links~ folder, and then finally reran the ~guix gc ...~
command. That was after doing a fsck as well.

Hat tip to Tobias for spending a good chunk of saturday helping me
through this. He though this might be related to issue 50121 after I
referred him to it.

Cheers,

Kyle

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

Toggle quote (7 lines)
> Am Dienstag, dem 31.05.2022 um 10:37 +0200 schrieb Maxime Devos:
>> (Is there a method to verify and repair a _single_ store item instead
>> of the whole store?).
> I think the syntax for that'd be ‘[sudo] guix build --repair
> STORE_ITEM’.
>
> Cheers
L
L
Ludovic Courtès wrote on 15 Jun 2022 22:40
control message for bug #55709
(address . control@debbugs.gnu.org)
87r13ppsmc.fsf@gnu.org
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